Strategies for Vaccine Design for Corona Virus for All Variants of Concern Using Immunoinformatics Techniques

Backgrounds: A short sequence of viral protein or peptide, can be used as a potential vaccine for the treatment of that virus. Considering all variants of concern (VOC), vaccine design with peptide for Severe Acute Respiratory Syndrome coronavirus ۲ (SARS CoV۲) is a challenging job for scientists. Materials & Methods: In this current study, an epitope containing peptide vaccine for nonstructural protein ۴ (nsp ۴) of SARS CoV۲ coronavirus has been predicted. With the help of a modified method for both B and T call epitope prediction, verified by molecular docking studies, linear B cell and T cell epitopes for nsp۴ protein, are predicted here. Predicted epitopes are analyzed further with population coverage calculation and epitope conservancy analysis. Findings: A short peptide sequence   ۷۴QRGGSYTNDKA۸۴  has been selected as B cell epitope considering the scores for surface accessibility, hydrophilicity, beta turn prediction for each amino acid residues. Similarly, the peptide sequences ۳۵۹ FLAHIQWMV۳۶۷ and   ۳۵۹ FLAHIQWVMFTPLV۳۷۳ are predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes can interest with HLA-A*۰۲:۰۱ and HLA-DRB*۰۱:۰۱, MHC allelic proteins respectively with lowest IC۵۰ values. Furthermore, no amino acid mutations are observed in GISAD Global initiate on sharing all influenza data) database for alpha, beta, gamma and delta variance of concerns (VOC). Among seven amino acid point mutation of nsp ۴ protein in Omicron variant, none of them is present in the peptide sequences of predicted epitope-based vaccines. Conclusion: The short peptide sequences can be predicted as vaccines to prevent coronavirus infections for all variants of concerns.

Keywords:

Peptide type vaccine design , COVID-۱۹ , B and T cell epitopes , MHC allelic protein , molecular docking study